So yeah, I think this explanation makes a lot more sense. I think it's much more likely that Nintendo has countermeasures already built in to handle manipulation of the operating system, and possibly something to handle a situation with a future 3DS flash cart. I can see them making the system "unplayable" if you mess with the system software or hardware (such as a mod chip). That's always been a risk factor any time we manipulate those things. Now, it's just possible that they have booby trapped it a bit.

It does go on to say that they can remove content that derived from using an unauthorized method from your system, and I'd wager that would mean save games, and possibly other benefits you might have obtained from using a cheat device or the like.

If you think about it, this explanation requires a LOT less reading between the lines.